Merge pull request #13 from zsloan/feature/add_rqtl_endpoints

Feature/add rqtl endpoints

1 files changed, 42 insertions, 0 deletions

diff --git a/tests/unit/computations/test_rqtl.py b/tests/unit/computations/test_rqtl.py
new file mode 100644
index 0000000..955d0ab
--- /dev/null
+++ b/tests/unit/computations/test_rqtl.py
@@ -0,0 +1,42 @@
+"""Test cases for procedures defined in computations.rqtl"""
+import unittest
+
+from unittest import mock
+from gn3.computations.rqtl import generate_rqtl_cmd
+
+class TestRqtl(unittest.TestCase):
+    """Test cases for computations.rqtl module"""
+    @mock.patch("gn3.computations.rqtl.generate_hash_of_string")
+    @mock.patch("gn3.computations.rqtl.get_hash_of_files")
+    def test_generate_rqtl_command(self, mock_get_hash_files, mock_generate_hash_string):
+        """Test computing mapping results with R/qtl"""
+        mock_get_hash_files.return_value = "my-hash1"
+        mock_generate_hash_string.return_value = "my-hash2"
+
+        self.assertEqual(
+            generate_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
+                              rqtl_wrapper_kwargs={
+                                  "g": "genofile",
+                                  "p": "phenofile",
+                                  "model": "normal",
+                                  "method": "hk",
+                                  "nperm": 1000,
+                                  "scale": "Mb",
+                                  "control": "rs123456"
+                              },
+                              rqtl_wrapper_bool_kwargs=[
+                                  "addcovar",
+                                  "interval"
+                              ]), {
+                                  "output_file":
+                                  "my-hash1my-hash2my-hash2-output.csv",
+                                  "rqtl_cmd": (
+                                      "Rscript rqtl-wrapper "
+                                      "--g genofile --p phenofile "
+                                      "--model normal --method hk "
+                                      "--nperm 1000 --scale Mb "
+                                      "--control rs123456 "
+                                      "--filename my-hash1my-hash2my-hash2-output.csv "
+                                      "--addcovar --interval"
+                                  )
+                              })